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Even code of a version can be selected and the contextual menu option "Copy" is enabled, code is not copied to the clipboard.
I stumbled upon the similar problem for *.js files with WTP and PDT installed in my IDE. Is in your case it is JavaScript files too or if not, then which file type is it? Also, Do you have WTP or PDT installed?
Cannot reproduce with anything except *.js files in Eclipse for PHP developers (there is WTP installed). No exceptions are logged, copying just does not work until you save the file version as a local one (using Save As option, then Copy into clipboard starts working just fine in the same editor). I'm sorry if I'm assigning the issue wrongly, but I just don't know exactly what is the component responsible for handling JavaScript files.